Reference Data with CVMFS without Ansible

Creative Commons License: CC-BY Questions:
  • Have an understanding of what CVMFS is and how it works

  • Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository

  • Configure your Galaxy to use these reference genomes and indices

Time estimation: 1 hour
Supporting Materials:
Last modification: Nov 21, 2023
License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License. The GTN Framework is licensed under MIT
purl PURL:
version Revision: 13


The CernVM-FS is a distributed filesystem perfectly designed for sharing readonly data across the globe. We use it in the Galaxy Project for sharing things that a lot of Galaxy servers need. Namely:

  • Reference Data
    • Genome sequences for hundreds of useful species.
    • Indices for the genome sequences
    • Various bioinformatic tool indices for the available genomes
  • Tool containers
    • Singularity containers of everything stored in Biocontainers (A bioinformatic tool container repository.) You get these for free every time you build a Bioconda recipe/package for a tool.
  • Others too..

From the Cern website:

The CernVM File System provides a scalable, reliable and low-maintenance software distribution service. It was developed to assist High Energy Physics (HEP) collaborations to deploy software on the worldwide-distributed computing infrastructure used to run data processing applications. CernVM-FS is implemented as a POSIX read-only file system in user space (a FUSE module). Files and directories are hosted on standard web servers and mounted in the universal namespace /cvmfs.”

A slideshow presentation on this subject is available. More details are available on (Galaxy Main’s) reference data setup and CVMFS system.

This exercise describes a manual process to install and configure CVMFS and Galaxy’s access to CVMFS. For a tutorial that uses Ansible to perform these tasks, see the Reference Data with CVMFS tutorial.

  1. Overview
  2. CVMFS and Galaxy without Ansible
    1. Configuring CVMFS
    2. Testing it out
    3. Look at the repository

CVMFS and Galaxy without Ansible

Comment: Manual version of Ansible Commands

If you wish to perform the same thing that we’ve just done, but by building the ansible script manually, follow these instructions. Otherwise, you have already done everything below and do not need to re-do it.

We are going to setup a CVMFS mount to the Galaxy reference data repository on our machines. To do this we have to install and configure the CVMFS client and then mount the appropriate CVMFS repository using the publicly available keys.

Hands-on: Installing the CVMFS Client
  1. On your remote machine, we need to first install the Cern software apt repo and then the CVMFS client and config utility:

    sudo apt install lsb-release
    sudo dpkg -i cvmfs-release-latest_all.deb
    rm -f cvmfs-release-latest_all.deb
    sudo apt-get update
    sudo apt install cvmfs cvmfs-config
  2. Now we need to run the CVMFS setup script.

    sudo cvmfs_config setup

Configuring CVMFS

The configuration is not complex for CVMFS:

Hands-on: Configuring CVMFS
  1. Create a /etc/cvmfs/default.local file with the following contents:


    This tells CVMFS to mount the Galaxy reference data repository and use a specific location for the cache which is limited to 500MB in size and to use the instance’s geo-location to choose the best CVMFS repo server to connect to. You can use the cvmfs_quota_limit role variable to control this setting.

In production uses 100GB, different sites have different needs and you can make your cache smaller depending on your usage. E.g. if your users only use one dataset from the reference data (e.g. just hg38) then perhaps you don’t need such a large cache.

  1. Create a /etc/cvmfs/domain.d/ file with the following contents:


    This is a list of the available stratum 1 servers that have this repo.

  2. Create a /etc/cvmfs/keys/ file with the following contents:

    -----BEGIN PUBLIC KEY-----
    -----END PUBLIC KEY-----
  3. Make a directory for the cache files

    sudo mkdir /srv/cvmfs

Testing it out

Probe the connection.

Hands-on: Testing it out
  1. Run sudo cvmfs_config probe


    What does it output?


    If this doesn’t return OK then you may need to restart autofs: sudo systemctl restart autofs

  2. Change directory into /cvmfs/ and list the files in that folder


    What do you see?

    You should see nothing, as CVMFS uses autofs in order to mount paths only upon request.

  3. Change directory into /cvmfs/

    Input: Bash
    cd /cvmfs/
    ls byhand
    ls managed

    What do you see now?

    You’ll see .loc files, genomes and indices. AutoFS only mounts the files when they’re accessed, so it appears like there is no folder there.

    And just like that we all have access to all the reference genomes and associated tool indices thanks to the Galaxy Project, IDC, and Nate’s hard work!

    If you are developing a new tool, and want to add a reference genome, we recommend you talk to us on Gitter. You can also look at one of the tools that uses reference data, and try and copy from that. If you’re developing the location files completely new, you need to write the data manager.

Look at the repository

Now to configure Galaxy to use the CVMFS references we have just installed, see the Ansible tutorial.